Project ID: plumID:23.028
Source: AIMD_simulation/plumed.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label calculates somethingHThe GROUP action with label H calculates the following quantities:| Quantity | Type | Description |
| H | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=9,10,11,12,13,14,15,16,27,28,31,32,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,147,148,149,150,155,156,157,158,161,162,167,168,169,170,175,176,177,178,181,182,183,184,189,190,191,192,197,198,258,259,260
NThe GROUP action with label N calculates the following quantities:| Quantity | Type | Description |
| N | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=17,18,19,20,21,22,23,24,25,26,29,30,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,151,152,153,154,159,160,163,164,165,166,171,172,173,174,179,180,185,186,187,188,193,194,195,196,199,200,201,202,257
LiThe GROUP action with label Li calculates the following quantities:| Quantity | Type | Description |
| Li | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-8:1,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
max_HThe COORDINATIONNUMBER action with label max_H calculates the following quantities:| Quantity | Type | Description |
| max_H | vector | the coordination numbers of the specified atoms |
| max_H_max | scalar | the maximum colvar |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=H SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Li,N SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.05}
# max_H: COORDINATIONNUMBER SPECIESA=H SPECIESB=Li,N SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.05}
max_H_grpThe GROUP action with label max_H_grp calculates the following quantities:| Quantity | Type | Description |
| max_H_grp | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=H
max_H_matThe CONTACT_MATRIX action with label max_H_mat calculates the following quantities:| Quantity | Type | Description |
| max_H_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=H GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=Li,N SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}
max_H_onesThe CONSTANT action with label max_H_ones calculates the following quantities:| Quantity | Type | Description |
| max_H_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=193
max_HThe MATRIX_VECTOR_PRODUCT action with label max_H calculates the following quantities:| Quantity | Type | Description |
| max_H | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=max_H_mat,max_H_ones
max_H_caverageThe MEAN action with label max_H_caverage calculates the following quantities:| Quantity | Type | Description |
| max_H_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=max_H PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_H_me_maxThe CUSTOM action with label max_H_me_max calculates the following quantities:| Quantity | Type | Description |
| max_H_me_max | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_H FUNCthe function you wish to evaluate=exp(x/0.05) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_H_mec_maxThe SUM action with label max_H_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_H_mec_max | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=max_H_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_H_maxThe CUSTOM action with label max_H_max calculates the following quantities:| Quantity | Type | Description |
| max_H_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_H_mec_max FUNCthe function you wish to evaluate=0.05*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
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ghostaThe FIXEDATOM action with label ghosta calculates the following quantities:| Quantity | Type | Description |
| ghosta | atoms | virtual atom calculated by FIXEDATOM action |
: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,20
ghosta: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,20 SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
NH3cThe COM action with label NH3c calculates the following quantities:| Quantity | Type | Description |
| NH3c | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=257-260
dNH3hostaThe DISTANCE action with label dNH3hosta calculates the following quantities:| Quantity | Type | Description |
| dNH3hosta.x | scalar | the x-component of the vector connecting the two atoms |
| dNH3hosta.y | scalar | the y-component of the vector connecting the two atoms |
| dNH3hosta.z | scalar | the z-component of the vector connecting the two atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ghosta,NH3c COMPONENTS calculate the x, y and z components of the distance separately and store them as label
abs_dNH3hostazThe MATHEVAL action with label abs_dNH3hostaz calculates the following quantities:| Quantity | Type | Description |
| abs_dNH3hostaz | scalar | an arbitrary function |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=dNH3hosta.z FUNCthe function you wish to evaluate=abs(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:| Quantity | Type | Description |
| uwall1.bias | scalar | the instantaneous value of the bias potential |
| uwall1.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=abs_dNH3hostaz ATthe positions of the wall=11.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes2The OPES_METAD action with label opes2 calculates the following quantities:| Quantity | Type | Description |
| opes2.bias | scalar | the instantaneous value of the bias potential |
| opes2.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes2.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes2.neff | scalar | effective sample size |
| opes2.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=max_H.max
PACEthe frequency for kernel deposition=50
BARRIERthe free energy barrier to be overcome=100
TEMP temperature=750
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes2
ARGthe labels of the scalars on which the bias will act=max_H.max
PACEthe frequency for kernel deposition=50
BARRIERthe free energy barrier to be overcome=100
TEMP temperature=750
SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
... OPES_METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=2
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=2
